Count bonds the correct number of times when calculating McGowan volume.
Methods for calculating k_diff, the diffusion factor, and the pre-exponential factor.

The diffusion factor is the effective rate constant divided by the intrinsic
rate constant. The pre-exponential factor, A, is decreased by the diffusion
factor.
Moved method for calculating Stokes-Einstein diffusivity.

This method is now in the solvation module instead of the Species class in model.py.